Use minnie_plotly_and_vtk_visualizer.ipynb
to generate a 2D and 3D interactive views of one or more cells of
interest from the minnie mm^3 volume. Uses matplotlib, plotly, and
vtk/openGL visualization methods. See an example visualization
below.
vtk visualization of neurons in the minnie volume
Use aibs_metamodel_celltypes_v661_v2_layer_positions.ipynb
to filter root ids of interest by cell classification (excitatory and
inhibitory), and subclasses, such as layer location for pyramidal
neurons and connectivity type for interneurons.
See chandelier
folder for visualization notebooks and renderings of select Chandelier
cells in the volume, highlighting the synaptic sites on to the initial
axon segment of target pyramidal neurons.
Chandelier-target neuron rendering
Use pyvista_decimate_mesh_cell_bodies_minnie.ipynb
to decimate cell meshes from the minnie volume. Default decimation
setting is 95%. You must first download the meshes to your local drive
using the minnie_plotly_and_vtk_visualizer.ipynb notebook.
Decimated files will be saved in the ‘/dec’ subdirectory. Note that
astrocyte meshes may take several hours to decimate. Most other cell
types will only take minutes.
Use vtk_decimated_cell_meshes_minnie.ipynb
to generate a 3D interactive view of one or more cells of interest using
decimated meshes from the minnie mm^3 volume. Uses vtk/openGL and has a
save view function. See an example visualization below.